Noely,
Within a single IAK file, you can have multiple FieldPoint modules on separate COM ports. There is no need to use separate IAKs for the program you are describing. Actually, older versions of NI-FieldPoint do not support having multiple IAKs in use simultaneously (I am not sure whether it is currently supported).
As for the Radio Modems, they are called SRM-6000s and can be used simultaneouslyon different serial ports. Although, using the SRM-6000 in a single master multi slave arrangement, you could use a single serial port to talk to both FP-1000s (3 SRMs total). You will need to configure the FP-1000s to have separate addresses (DIP Switch setting).
Regards,
Aaron
LabVIEW Champion, CLA, CPI